Exploring
DNA

Explore DNA structure by reading the text below and clicking the accompanying blue buttons. At any point, you can click and drag the molecule to move it yourself (see the "Help" button, above left, for more ways to manipulate the molecule). "Movie" buttons play a short animation; to skip to the end of the animation, click on the "Jump to final view" button instead.

The opening view of DNA is based on Figure 4-7(A) in Stryer's Biochemistry (4th Edition). To begin exploring DNA, first get a feel for its structure in three dimensions--click and drag the structure to make it move. If you'd like practice controlling the 3D movement, look at the view in Figure 4-7(B) and try to orient the molecule in precisely the same way.


The Double Helix

DNA is composed of intertwining strands of nucleotides. Each strand is a helix, that is, each is shaped like a spiral staircase. The two strands bound together make DNA a double helix.

Molecules of DNA in living cells are very, very long--the model shown here is just a short fragment, only a tiny fraction of the length of the DNA molecules in a living organism.

View each strand separately:

Strand A (green original):
Strand B (red original):
Restore both strands:

A skeleton of covalent bonds holds the atoms of the double helix together. (In this view, atoms are colored by element: C, N, O, P.):

To get a closer look at the covalent bonds, zoom in and out by shift-clicking (see Help), or by using these buttons:

Zoom in:
Zoom out:

Each strand has two components:

The bases:
The backbone:
Restore both:

Change views:

Spacefill:
Ball and stick:
Sticks:

Color by atom, one element at a time:

Carbon
Nitrogen
Oxygen
Phosphorus
Restore all:

Explore the Backbone

The backbone is composed of alternating sugar (deoxyribose) and phosphate groups:

DNA: "D" is for deoxyribose

The carbons of the deoxyribose sugar ring are numbered. ("Prime" symbols after the numbers distinguish sugar atoms from the atoms in purine/pyrimidine bases, which take "unprimed" numbers.):

Movie:
Jump to final view:

Replace numbered sugar in backbone:

The sugar is attached to phosphates at its 3' and 5' carbons:

A phosphodiester bridge links the 5' hydroxyl of each sugar to the 3' hydroxyl of the next:
Jump to final view:

If you haven't done so already, rotate the molecule to explore the relationship of the numbered sugar atoms to the backbone.

The sugars on opposite strands are oriented in opposite (antiparallel) directions:
Jump to final view:

The 5' carbons point in opposite directions on the two strands:

Each strand of DNA is said to have a 5' end and a 3' end, based on the orientation of its deoxyribose sugars:


Explore the Base Pairs

Adenine-thymine base pair
(compare Figure 4-9 in the text)

Movie:
Jump to final view:

The atoms on the rings of the bases are numbered:

Bases attach to their respective backbones by forming bonds with 1' carbons of backbone sugars:

Attach the sugars to the bases:

Number the sugar carbons:

Attach the phosphates to the 5' and 3' hydroxyls:

Explore this view, using the mouse to move the structure. Ask yourself:
What's the approximate angle between the planes of the bases and the planes of their adjacent sugar rings?

Now add the bases immediately above and below the A·T base pair:

The present view nearly duplicates that of Figure 4-12 in the text. Explore this view using the mouse, asking yourself:
How is the central base pair oriented with respect to ones above and below it?

Cytosine-guanine base pair
(compare Figure 4-10 in the text)

Movie:
Jump to final view:

Number the base ring atoms:

Add the 1' sugar carbons:


What Holds the Two Strands Together?

Two noncovalent forces stabilize the double helix.

1. The most widely discussed is hydrogen bonding between base pairs. Cytosine and guanine form three hydrogen bonds; adenine and thymine form only two:

Although individual hydrogen bonds are very weak, the combined force of all the hydrogen bonds between the two strands helps to stabilize the double helix:
Movie:
Jump to final view:

2."Base stacking" is another factor in helix stability. Hydrophobic interactions between nucleotide bases (non-polar structures) and the watery environment of the cell encourage the bases to stack one above the other, minimizing their contact with water.

Weak, but numerous van der Waals interactions arise between the atoms of adjacent bases, increasing the stability of the double helix.

Return to full model in spacefill:

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